SA's Water Minister has launched a scathing attack of the New South Wales Government's conduct of Murray-Darling Basin water management and repeated calls for a judicial inquiry.

The ABC's Four Corners program last night revealed allegations of some irrigators using meter tampering and improper record-keeping to pump billions of litres of water earmarked for the environment onto cotton farms in far west New South Wales.

SA Water Minister Ian Hunter said he was "shocked" at the extent of water theft and allegations of water tampering "and the way it has been systematically endorsed across a whole region of New South Wales".

"I was incredibly upset and disappointed that it appears that at a very senior level in the public service, people knew about it and determined to turn a blind eye to it," he said.

"And more than that, disbanded that compliance unit that was responsible for checking on these things.

"If nothing else, that requires a judicial inquiry."

He said there had been no leadership from the Federal Government in response to the findings and called for an urgent COAG meeting.

Gloria Jones, from a fishing family at Clayton Bay, said the plan should be delivered in full and urged irrigators to think about the system's health.

She said she was not surprised by last night's ABC story because "we always knew that water wasn't coming down the Darling".

"I felt it took Four Corners to take it into the living rooms of the people in Sydney and Melbourne and Adelaide who don't get the opportunity to go to the Darling and actually see what's happening. It's a place a bit too far away for most people."

Irrigators 'unfairly' made targets

Meanwhile, the National Irrigators Council said the Four Corners' allegations had demonised irrigators and unfairly painted the Basin Plan as a failure.

Chairman Gavin McMahon said the program had unfairly represented irrigators as doing the wrong thing, when the majority were complying with restrictions on their water use and "striving for excellence".

"I was a little disappointed with the program and particularly the conclusions that it drew," he said.

"It was talking about [allegations of] illegal water use in the Barwon river system ... and drew conclusions about the failure of the Basin Plan ... that weren't really backed up by evidence.

"I'm sure some of the [issues raised] are real but that's really now up to the New South Wales Government to take on board and address those issues."

He said the program had made the MDBP out as ineffective but in reality it was delivering real benefits to downstream communities and its value should not be underestimated.

"From where we are [in the Riverland], the Basin Plan is running reasonably well [and] we're certainly starting to see some benefits ... on the river floodplains here," he said.

Riverland self-described "green irrigator" Bruce Hewitt said he was "heartbroken" by the allegations of improper water use.